RESUMO
Current Genome-Wide Association Studies (GWAS) rely on genotype imputation to increase statistical power, improve fine-mapping of association signals, and facilitate meta-analyses. Due to the complex demographic history of Latin America and the lack of balanced representation of Native American genomes in current imputation panels, the discovery of locally relevant disease variants is likely to be missed, limiting the scope and impact of biomedical research in these populations. Therefore, the necessity of better diversity representation in genomic databases is a scientific imperative. Here, we expand the 1,000 Genomes reference panel (1KGP) with 134 Native American genomes (1KGP + NAT) to assess imputation performance in Latin American individuals of mixed ancestry. Our panel increased the number of SNPs above the GWAS quality threshold, thus improving statistical power for association studies in the region. It also increased imputation accuracy, particularly in low-frequency variants segregating in Native American ancestry tracts. The improvement is subtle but consistent across countries and proportional to the number of genomes added from local source populations. To project the potential improvement with a higher number of reference genomes, we performed simulations and found that at least 3,000 Native American genomes are needed to equal the imputation performance of variants in European ancestry tracts. This reflects the concerning imbalance of diversity in current references and highlights the contribution of our work to reducing it while complementing efforts to improve global equity in genomic research.
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A shift in environmental conditions impacts the evolution of complex developmental and behavioral traits. The Mexican cavefish, Astyanax mexicanus, is a powerful model for examining the evolution of development, physiology, and behavior because multiple cavefish populations can be compared to an extant, ancestral-like surface population of the same species. Many behaviors have diverged in cave populations of A. mexicanus, and previous studies have shown that cavefish have a loss of sleep, reduced stress, an absence of social behaviors, and hyperphagia. Despite these findings, surprisingly little is known about the changes in neuroanatomy that underlie these behavioral phenotypes. Here, we use serial sectioning to generate brain atlases of surface fish and three independent cavefish populations. Volumetric reconstruction of serial-sectioned brains confirms convergent evolution on reduced optic tectum volume in all cavefish populations tested. In addition, we quantified volumes of specific neuroanatomical loci within several brain regions that have previously been implicated in behavioral regulation, including the hypothalamus, thalamus, and habenula. These analyses reveal an enlargement of the hypothalamus in all cavefish populations relative to surface fish, as well as subnuclei-specific differences within the thalamus and prethalamus. Taken together, these analyses support the notion that changes in environmental conditions are accompanied by neuroanatomical changes in brain structures associated with behavior. This atlas provides a resource for comparative neuroanatomy of additional brain regions and the opportunity to associate brain anatomy with evolved changes in behavior.
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The therapeutic effects of drugs are well known to result from their interaction with multiple intracellular targets. Accordingly, the pharma industry is currently moving from a reductionist approach based on a 'one-target fixation' to a holistic multitarget approach. However, many drug discovery practices are still procedural abstractions resulting from the attempt to understand and address the action of biologically active compounds while preventing adverse effects. Here, we discuss how drug discovery can benefit from the principles of evolutionary biology and report two real-life case studies. We do so by focusing on the desirability principle, and its many features and applications, such as machine learning-based multicriteria virtual screening.
Assuntos
Descoberta de Drogas/métodos , Evolução Biológica , Desenho de Fármacos , HumanosRESUMO
Dengue fever is a major public health problem worldwide, caused by any of four virus (DENV-1, DENV-2, DENV-3 and DENV-4; Flaviviridae: Flavivirus), transmitted by Aedes aegypti mosquito. Reducing the levels of infestation by A. aegypti is one ofthe few current strategies to control dengue fever. Entomological indicators are used by dengue national control program to measure the infestation of A. aegypti, but little is known about predictive power of these indicators to measure dengue risk. In this spatial case-control study, we analyzed the spatial distribution of the risk of dengue and the influence of entomological indicators of A. aegypti in its egg, larva-pupa and adult stages occurring in a mid-size city in the state of São Paulo. The dengue cases were those confirmed by the citys epidemiological surveillance system and the controls were obtained through random selection of points within the perimeter of the inhabited area. The values of the entomological indicators were extrapolated for the entire study area through the geostatistical ordinary kriging technique. For each case and control, the respective indicator values were obtained, according with its geographical coordinates and analyzed by using a generalized additive model. Dengue incidence demonstrated a seasonal behavior, as well as the entomological indicators of all mosquitos evolutionary stages...
Assuntos
Humanos , Animais , Dengue/diagnóstico , Dengue/epidemiologia , Dengue/transmissãoRESUMO
OBJECTIVES: To compare the neurocognitive outcomes of patients with phenylketonuria (PKU) to determine whether decreasing phenylalanine (Phe) levels to <240 is preferable to the use of 360 µmol/L as an upper-target Phe level. An additional aim was to establish the influence of biochemical indices other than Phe on neurocognitive outcomes. STUDY DESIGN: Patients with PKU (n = 63; mean age 10.8 ± 2.3 years) and healthy controls (n = 73; mean age 10.9 ± 2.2 years) performed computerized tasks measuring neurocognitive functions (inhibitory control, cognitive flexibility, and motor control). Lifetime and concurrent blood Phe levels, Phe-to-tyrosine ratio (Phe:Tyr), and Phe variations were examined in relation to neurocognitive outcomes using nonparametric tests and regression analyses. RESULTS: Patients with PKU with Phe levels ≤240 µmol/L and healthy controls performed equally well. Patients with Phe levels between 240 and 360 µmol/L and ≥360 µmol/L performed more poorly than did controls across tasks. Patients with Phe levels ≤240 µmol/L performed significantly better than patients with levels between 240 and 360 µmol/L on tasks measuring inhibitory control and cognitive flexibility. Absolute Phe levels and Phe variation were the best predictors of motor control, whereas Phe:Tyr were the best predictors of inhibitory control. CONCLUSIONS: The results of this study suggest that upper Phe targets should be lowered to optimize neurocognitive outcomes. Moreover, Phe variation and Phe:Tyr appear to be of additional value in treatment monitoring.
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Fenilcetonúrias/tratamento farmacológico , Fenilcetonúrias/fisiopatologia , Adolescente , Criança , Feminino , Humanos , Masculino , Testes Neuropsicológicos , Fenilalanina/sangue , Fenilcetonúrias/sangue , Guias de Prática Clínica como Assunto , Tirosina/sangueAssuntos
Idoso , Humanos , Masculino , Pessoa de Meia-Idade , Imageamento por Ressonância Magnética/métodos , Neoplasias da Próstata/diagnóstico , Cirurgia Assistida por Computador/métodos , Ultrassonografia de Intervenção/métodos , Reprodutibilidade dos Testes , Reto , Sensibilidade e EspecificidadeRESUMO
The subseafloor marine biosphere may be one of the largest reservoirs of microbial biomass on Earth and has recently been the subject of debate in terms of the composition of its microbial inhabitants, particularly on sediments from the Peru Margin. A metagenomic analysis was made by using whole-genome amplification and pyrosequencing of sediments from Ocean Drilling Program Site 1229 on the Peru Margin to further explore the microbial diversity and overall community composition within this environment. A total of 61.9 Mb of genetic material was sequenced from sediments at horizons 1, 16, 32, and 50 m below the seafloor. These depths include sediments from both primarily sulfate-reducing methane-generating regions of the sediment column. Many genes of the annotated genes, including those encoding ribosomal proteins, corresponded to those from the Chloroflexi and Euryarchaeota. However, analysis of the 16S small-subunit ribosomal genes suggests that Crenarchaeota are the abundant microbial member. Quantitative PCR confirms that uncultivated Crenarchaeota are indeed a major microbial group in these subsurface samples. These findings show that the marine subsurface is a distinct microbial habitat and is different from environments studied by metagenomics, especially because of the predominance of uncultivated archaeal groups.
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Archaea/genética , Bactérias/genética , Sedimentos Geológicos/microbiologia , Água do Mar/microbiologia , Archaea/classificação , Bactérias/classificação , DNA Arqueal/genética , DNA Bacteriano/genética , Geografia , Peru , Filogenia , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Microbiologia da ÁguaRESUMO
The complete genome sequences of hepatitis D virus (HDV) strains isolated from three Yucpa Amerindians in Venezuela were determined and found to be genotype III. Comparison of these three genotype III sequences demonstrated the presence of a hypervariable region containing numerous substitutions, insertions/deletions and a highly conserved region containing the self-cleavage domains, which have been reported previously for genotypes I and II. Amino acid changes within the first 90 amino acids of the hepatitis D antigen (HDAg) were found in the genotype III sequences, while the remainder of the HDAg-coding sequence was conserved. The secondary structure for the RNA-editing site differed between genotypes I and III. It was concluded that the serious delta hepatitis outbreaks characterized epidemiologically in the Yucpa Amerindians were caused by HDV genotype III isolates that were related to HDV genotype III isolates from other regions of South America.
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Vírus Delta da Hepatite/classificação , Sequência de Aminoácidos , Genótipo , Vírus Delta da Hepatite/genética , Indígenas Sul-Americanos , Dados de Sequência Molecular , Filogenia , Edição de RNA , VenezuelaRESUMO
The complete genome sequences of hepatitis B virus (HBV) from 12 HBV-infected Yucpa Indians of Venezuela, a group with highly endemic HBV, were amplified and sequenced. The 12 isolates were closely related to each other, with 98.6-100% nucleotide identity. A phylogenetic tree based on the complete genome indicated clearly that they were genotype F. Three individuals had evidence of infection with two different HBV deletion mutants. In two individuals, a three amino acid deletion was identified just prior to the 'a' determinant loop of the S region. A third individual was infected with virus that contained a complete core reading frame and a population that contained a deletion in the middle of the core region. These results indicate that genotype F HBV is present in the Venezuelan Yucpa Amerindians and the complete genome sequence allowed the identification of two unique deletion mutants in a limited set of samples.
Assuntos
Genoma Viral , Vírus da Hepatite B/genética , Hepatite B/virologia , Indígenas Sul-Americanos , Sequência de Aminoácidos , Sequência Consenso , Genótipo , Hepatite B/epidemiologia , Antígenos de Superfície da Hepatite B/química , Antígenos de Superfície da Hepatite B/genética , Vírus da Hepatite B/química , Vírus da Hepatite B/classificação , Humanos , Dados de Sequência Molecular , Filogenia , Alinhamento de Sequência , Deleção de Sequência/genética , Venezuela/epidemiologia , Proteínas Virais/química , Proteínas Virais/genéticaRESUMO
Angiogenesis, the sprouting of new blood vessels from pre-existing vessels, is a complex, multicellular phenomenon involving capillary endothelial cell (EC) proliferation, migration, and tissue infiltration. The elucidation of the biochemical and molecular factors which control angiogenesis is fundamental to our understanding of normal blood vessel development, as well as of the pathogenesis of abnormal blood vessel formation. Angiogenesis is associated with numerous physiological processes, including embryogenesis, wound healing, organ regeneration, and the female reproductive cycle. However, abnormal angiogenesis also plays a major role in the pathogenesis of tumor growth, rheumatoid arthritis, atherosclerosis and various retinopathies. The cellular and molecular mechanisms underlying both physiological and pathophysiological angiogenesis are only now beginning to be understood. Vascular endothelial growth factor was initially discovered as an unidentified tumor-derived factor which increased microvascular permeability (vascular permeability factor, VPF). Subsequently, it was determined that the protein exhibited mitogenic effects on endothelial cells, but not other cell types. Multiple receptor subtypes have been described which may in part explain the multiplicity of biological actions that have been ascribed to VEGF/VPF in the literature. In this overview, we briefly summarize what is currently known about VEGF and VEGF receptor biology, as well as VEGF receptor signal transduction mechanisms in endothelial cells.
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Indutores da Angiogênese/fisiologia , Sequência de Aminoácidos , Indutores da Angiogênese/química , Endotélio Vascular/efeitos dos fármacos , Éxons/genética , Feminino , Regulação da Expressão Gênica/genética , Humanos , Masculino , Dados de Sequência Molecular , Peso Molecular , Receptores de Fatores de Crescimento/química , Receptores de Fatores de Crescimento/fisiologia , Transdução de SinaisRESUMO
Angiogenesis, the sprouting of new blood vessels from pre-existing vessels, is a complex, multicellular phenomenon involving capillary endothelial cell (EC) proliferation, migration, and tissue infiltration. The elucidation of the biochemical and molecular factors which control angiogenesis is fundamental to our understanding of normal blood vessel development, as well as of the pathogenesis of abnormal blood vessel formation. Angiogenesis is associated with numerous physiological processes, including embryogenesis, wound healing, organ regeneration, and the female reproductive cycle. However, abnormal angiogenesis also plays a major role in the pathogenesis of tumor growth, rheumatoid arthritis, atherosclerosis and various retinopathies. The cellular and molecular mechanisms underlying both physiological and pathophysiological angiogenesis are only now beginning to be understood. Vascular endothelial growth factor was initially discovered as an unidentified tumor-derived factor which increased microvascular permeability (vascular permeability factor, VPF). Subsequently, it was determined that the protein exhibited mitogenic effects on endothelial cells, but not other cell types. Multiple receptor subtypes have been described which may in part explain the multiplicity of biological actions that have been ascribed to VEGF/VPF in the literature. In this overview, we briefly summarize what is currently known about VEGF and VEGF receptor biology, as well as VEGF receptor signal transduction mechanisms in endothelial cells